[gmx-users] g_rdf graph edges

hi all i encounter a Fatal error: More than 4 graph edges per atom when using g_rdf on a trajectory that was generated using 'pbc=full'. berk hess correctly stated that pbc=full circumvents this problem in mdrun, but i've not seen any news of this behaviour with the analysis programs. has

Re: [gmx-users] g_rdf graph edges

Manohar Murthi wrote: hi all i encounter a Fatal error: More than 4 graph edges per atom when using g_rdf on a trajectory that was generated using 'pbc=full'. berk hess correctly stated that pbc=full circumvents this problem in mdrun, but i've not seen any news of this behaviour with the

Re: [gmx-users] make template

Stephan Mackowiak wrote: Hi, I tried to compile file template.c in the folder share/template and the response is nothing to be done for all. The suggestion on the mail list copying template.c to subdir tools, doing automake and ./config is not working in my case. When I

[gmx-users] position restrained energy minimization

Hello gmx-users! 1. Is it possible to perform position restrained energy minimisation? 2. If so what are the parameter that I need to incorporate in the em.mdp file. By just changing the define = -DFLEX_SPC in the em.mdp to define = -DPOSRES will it mean that I am now entering into position

[gmx-users] segmentation fault with fitted gro files

Dear all, I am running a series of AFM simulations starting from different conformations taken from a trajectory (gmx 3.3). Everything works fine, but if I try to orient all the snapshots with respect to a reference (based on the protein superimposition) I get segmentation fault for all of

[gmx-users] how to use g_sham ?

Dear all users : g_sham is a new program in 3.3 and i cant find any discussion about how to use in mailing lists, and i didnt catch the pointaboutthe instructionsin user manual. Is it possible to draw pics about PMF or free energy landscape using some special coordinates, like RMSD,